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callahantiff / PheKnowLator

PheKnowLator: Heterogeneous Biomedical Knowledge Graphs and Benchmarks Constructed Under Alternative Semantic Models
https://github.com/callahantiff/PheKnowLator/wiki
Apache License 2.0
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Resolving Issue 116 #117

Closed callahantiff closed 2 years ago

callahantiff commented 2 years ago

Purpose

As pointed out in issue #116 an issue with writing out metadata to a flat-file was discovered and the root cause was the presence of \n characters in long strings obtained from the ontologies. The solution was to check all strings before writing them out to ensure that the characters were removed.

Output impacted

There is a fix underway to update and fix all archived output to address this error.

sonarcloud[bot] commented 2 years ago

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 3 Code Smells

93.8% 93.8% Coverage
0.0% 0.0% Duplication

callahantiff commented 2 years ago

@ChuckKollar - Just wanted to call to your attention this PR, which resulted in some minor changes to the notebooks/OWLNETS_Example_Application.ipynb file. See here for details. I am happy to make a PR to your repos in the future for changes like this if that would be helpful. Just let me know! 😄

callahantiff commented 2 years ago

Solution for Existing Files: The Gist used to update and fix the node_metadata_dict.pkl and XXXX_NodeLabels.txt files for all v2.0.0 (excluding build_10MAY2020), v2.1.0, and v3.0.0 builds can be found here: https://gist.github.com/callahantiff/f31a936d967c8f44d5d0e51c563ae65f